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de Souza PVS, Serrano PDL, Farias IB, Machado RIL, Badia BDML, de Oliveira HB, Barbosa AS, Pereira CA, Moreira VDF, Chieia MAT, Barbosa AR, Braga VL, Pinto WBVDR, Oliveira ASB. Clinical and Genetic Aspects of Juvenile Amyotrophic Lateral Sclerosis: A Promising Era Emerges. Genes (Basel) 2024; 15:311. [PMID: 38540369 PMCID: PMC10969870 DOI: 10.3390/genes15030311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 06/14/2024] Open
Abstract
Juvenile Amyotrophic Lateral Sclerosis is a genetically heterogeneous neurodegenerative disorder, which is frequently misdiagnosed due to low clinical suspicion and little knowledge about disease characteristics. More than 20 different genetic loci have been associated with both sporadic and familial juvenile Amyotrophic Lateral Sclerosis. Currently, almost 40% of cases have an identifiable monogenic basis; type 6, associated with FUS gene variants, is the most prevalent globally. Despite several upper motor neuron-dominant forms being generally associated with long-standing motor symptoms and slowly progressive course, certain subtypes with lower motor neuron-dominant features and early bulbar compromise lead to rapidly progressive motor handicap. For some monogenic forms, there is a well-established genotypic-phenotypic correlation. There are no specific biochemical and neuroimaging biomarkers for the diagnosis of juvenile Amyotrophic Lateral Sclerosis. There are several inherited neurodegenerative and neurometabolic disorders which can lead to the signs of motor neuron impairment. This review emphasizes the importance of high clinical suspicion, assessment, and proper diagnostic work-up for juvenile Amyotrophic Lateral Sclerosis.
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Affiliation(s)
- Paulo Victor Sgobbi de Souza
- Motor Neuron Disease Unit, Division of Neuromuscular Diseases, Federal University of Sao Paulo (UNIFESP), Sao Paulo 04039-060, Brazil; (P.d.L.S.); (W.B.V.d.R.P.)
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Lattante S, Marangi G, Doronzio PN, Conte A, Bisogni G, Zollino M, Sabatelli M. High-Throughput Genetic Testing in ALS: The Challenging Path of Variant Classification Considering the ACMG Guidelines. Genes (Basel) 2020; 11:genes11101123. [PMID: 32987860 PMCID: PMC7600768 DOI: 10.3390/genes11101123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
The development of high-throughput sequencing technologies and screening of big patient cohorts with familial and sporadic amyotrophic lateral sclerosis (ALS) led to the identification of a significant number of genetic variants, which are sometimes difficult to interpret. The American College of Medical Genetics and Genomics (ACMG) provided guidelines to help molecular geneticists and pathologists to interpret variants found in laboratory testing. We assessed the application of the ACMG criteria to ALS-related variants, combining data from literature with our experience. We analyzed a cohort of 498 ALS patients using massive parallel sequencing of ALS-associated genes and identified 280 variants with a minor allele frequency < 1%. Examining all variants using the ACMG criteria, thus considering the type of variant, inheritance, familial segregation, and possible functional studies, we classified 20 variants as “pathogenic”. In conclusion, ALS’s genetic complexity, such as oligogenic inheritance, presence of genes acting as risk factors, and reduced penetrance, needs to be considered when interpreting variants. The goal of this work is to provide helpful suggestions to geneticists and clinicians dealing with ALS.
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Affiliation(s)
- Serena Lattante
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Faculty of Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Roma, Italy; (S.L.); (P.N.D.); (M.Z.)
- Complex Operational Unit of Medical Genetics, Department of Laboratory and Infectious Disease Sciences, A. Gemelli University Hospital Foundation IRCCS, 00168 Roma, Italy
| | - Giuseppe Marangi
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Faculty of Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Roma, Italy; (S.L.); (P.N.D.); (M.Z.)
- Complex Operational Unit of Medical Genetics, Department of Laboratory and Infectious Disease Sciences, A. Gemelli University Hospital Foundation IRCCS, 00168 Roma, Italy
- Correspondence: ; Tel.: +39-0630154606
| | - Paolo Niccolò Doronzio
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Faculty of Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Roma, Italy; (S.L.); (P.N.D.); (M.Z.)
- Complex Operational Unit of Medical Genetics, Department of Laboratory and Infectious Disease Sciences, A. Gemelli University Hospital Foundation IRCCS, 00168 Roma, Italy
| | - Amelia Conte
- Adult NEMO Clinical Center, Complex Operational Unit of Neurology, Department of Aging, Neurological, Orthopedic and Head-Neck Sciences, A. Gemelli University Hospital Foundation IRCCS, 00168 Roma, Italy; (A.C.); (G.B.); (M.S.)
| | - Giulia Bisogni
- Adult NEMO Clinical Center, Complex Operational Unit of Neurology, Department of Aging, Neurological, Orthopedic and Head-Neck Sciences, A. Gemelli University Hospital Foundation IRCCS, 00168 Roma, Italy; (A.C.); (G.B.); (M.S.)
| | - Marcella Zollino
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Faculty of Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Roma, Italy; (S.L.); (P.N.D.); (M.Z.)
- Complex Operational Unit of Medical Genetics, Department of Laboratory and Infectious Disease Sciences, A. Gemelli University Hospital Foundation IRCCS, 00168 Roma, Italy
| | - Mario Sabatelli
- Adult NEMO Clinical Center, Complex Operational Unit of Neurology, Department of Aging, Neurological, Orthopedic and Head-Neck Sciences, A. Gemelli University Hospital Foundation IRCCS, 00168 Roma, Italy; (A.C.); (G.B.); (M.S.)
- Section of Neurology, Department of Neuroscience, Faculty of Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Roma, Italy
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Davi C, Pastor A, Oliveira T, Neto FBDL, Braga-Neto U, Bigham AW, Bamshad M, Marques ETA, Acioli-Santos B. Severe Dengue Prognosis Using Human Genome Data and Machine Learning. IEEE Trans Biomed Eng 2019; 66:2861-2868. [PMID: 30716030 DOI: 10.1109/tbme.2019.2897285] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Dengue has become one of the most important worldwide arthropod-borne diseases. Dengue phenotypes are based on laboratorial and clinical exams, which are known to be inaccurate. OBJECTIVE We present a machine learning approach for the prediction of dengue fever severity based solely on human genome data. METHODS One hundred and two Brazilian dengue patients and controls were genotyped for 322 innate immunity single nucleotide polymorphisms (SNPs). Our model uses a support vector machine algorithm to find the optimal loci classification subset and then an artificial neural network (ANN) is used to classify patients into dengue fever or severe dengue. RESULTS The ANN trained on 13 key immune SNPs selected under dominant or recessive models produced median values of accuracy greater than 86%, and sensitivity and specificity over 98% and 51%, respectively. CONCLUSION The proposed classification method, using only genome markers, can be used to identify individuals at high risk for developing the severe dengue phenotype even in uninfected conditions. SIGNIFICANCE Our results suggest that the genetic context is a key element in phenotype definition in dengue. The methodology proposed here is extendable to other Mendelian based and genetically influenced diseases.
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